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jlbuerer / LaMIRA

Lariat Mapping by Inverted Read Alignment
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bash map_lariats.sh failed #9

Open santataRU opened 7 months ago

santataRU commented 7 months ago

Dear Developer,

I downloaded the code and tried to run it but failed with the message below: Command line: bash map_lariats.sh /Users/bieniaszlab/Documents/Xiao/Peng_Zhang/test_examples/5ss_mut/5ss_test_WT.fq 197 /Users/bieniaszlab/Documents/Xiao/CLIP/index/hg38/bowtieindex/hg38_genome /Users/bieniaszlab/Documents/Xiao/CLIP/index/hg38/Homo_sapiens.GRCh38.108.sorted.gtf 1 ~/Desktop

Error message: python3: can't open file '/Users/bieniaszlab/Downloads/LaMIRA-master/./mapping_scripts/create_SS_and_intron_tables.py': [Errno 2] No such file or directory Can't locate aligner.pm in @INC (you may need to install the aligner module) (@INC contains: ./ /Users/bieniaszlab/opt/miniconda3/lib/site_perl/5.26.2/darwin-thread-multi-2level /Users/bieniaszlab/opt/miniconda3/lib/site_perl/5.26.2 /Users/bieniaszlab/opt/miniconda3/lib/5.26.2/darwin-thread-multi-2level /Users/bieniaszlab/opt/miniconda3/lib/5.26.2 .) at ./mapping_scripts/find_lariats.pl line 7. BEGIN failed--compilation aborted at ./mapping_scripts/find_lariats.pl line 7.

I appreciate it if there is any input.

Regards,

Xiao

santataRU commented 7 months ago

map_lariats.sh line 39 python3 ./mapping_scripts/create_SS_and_intron_tables.py should be python3 ./mapping_scripts/create_SS_and_intron_table.py. This causes "[Errno 2] No such file or directory.

jlbuerer commented 7 months ago

Yes, sorry there appears to be an error with the relative paths here. However, I do not maintain this version of the lariat mapping code. I would suggest you use lariat_mapping instead

santataRU commented 6 months ago

Thank you for the suggestions!